{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T13:56:26Z","timestamp":1777470986842,"version":"3.51.4"},"reference-count":36,"publisher":"Springer Science and Business Media LLC","issue":"S3","license":[{"start":{"date-parts":[[2019,3,1]],"date-time":"2019-03-01T00:00:00Z","timestamp":1551398400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2019,3]]},"DOI":"10.1186\/s12859-019-2649-0","type":"journal-article","created":{"date-parts":[[2019,3,29]],"date-time":"2019-03-29T09:02:49Z","timestamp":1553850169000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Protein complex detection based on flower pollination mechanism in multi-relation reconstructed dynamic protein networks"],"prefix":"10.1186","volume":"20","author":[{"given":"Xiujuan","family":"Lei","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ming","family":"Fang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ling","family":"Guo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fang-Xiang","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,3,29]]},"reference":[{"issue":"6887","key":"2649_CR1","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1038\/nature750","volume":"417","author":"C Mering von","year":"2002","unstructured":"von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature. 2002;417(6887):399\u2013403.","journal-title":"Nature"},{"issue":"6","key":"2649_CR2","doi-asserted-by":"publisher","first-page":"e1000807","DOI":"10.1371\/journal.pcbi.1000807","volume":"6","author":"J Las Rivas De","year":"2010","unstructured":"De Las Rivas J, Fontanillo C. Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. PLoS Comput Biol. 2010;6(6):e1000807.","journal-title":"PLoS Comput Biol"},{"key":"2649_CR3","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1186\/1471-2105-4-2","volume":"4","author":"GD Bader","year":"2003","unstructured":"Bader GD, Hogue CWV. An automated method for finding molecular complexes in large protein interaction networks. BMC bioinformatics. 2003;4:2\u20132.","journal-title":"BMC bioinformatics"},{"issue":"5","key":"2649_CR4","doi-asserted-by":"publisher","first-page":"471","DOI":"10.1038\/nmeth.1938","volume":"9","author":"T Nepusz","year":"2012","unstructured":"Nepusz T, Yu H, Paccanaro A. Detecting overlapping protein complexes in protein-protein interaction networks. Nat Methods. 2012;9(5):471\u2013U481.","journal-title":"Nat Methods"},{"issue":"15","key":"2649_CR5","doi-asserted-by":"publisher","first-page":"1891","DOI":"10.1093\/bioinformatics\/btp311","volume":"25","author":"G Liu","year":"2009","unstructured":"Liu G, Wong L, Chua HN. Complex discovery from weighted PPI networks. Bioinformatics. 2009;25(15):1891\u20137.","journal-title":"Bioinformatics"},{"key":"2649_CR6","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1016\/j.ins.2017.10.013","volume":"425","author":"X Lei","year":"2018","unstructured":"Lei X, Zhang Y, Cheng S, Wu F-X, Pedrycz W. Topology potential based seed-growth method to identify protein complexes on dynamic PPI data. Inf Sci. 2018;425:140\u201353.","journal-title":"Inf Sci"},{"issue":"11","key":"2649_CR7","doi-asserted-by":"crossref","first-page":"1681","DOI":"10.1093\/bioinformatics\/btx043","volume":"33","author":"C-Y Ma","year":"2017","unstructured":"Ma C-Y, Y-PP C, Berger B, Liao C-S. Identification of protein complexes by integrating multiple alignment of protein interaction networks. Bioinformatics. 2017;33(11):1681\u20138.","journal-title":"Bioinformatics"},{"key":"2649_CR8","first-page":"265","volume":"6","author":"P Lecca","year":"2015","unstructured":"Lecca P, Re A. Detecting modules in biological networks by edge weight clustering and entropy significance. Front Genet. 2015;6:265.","journal-title":"Front Genet"},{"key":"2649_CR9","unstructured":"Van Dongen S. Graph clustering by flow simulation: Phd thesis University of Utrecht; 2000."},{"key":"2649_CR10","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1016\/j.ins.2015.09.028","volume":"329","author":"X Lei","year":"2016","unstructured":"Lei X, Wang F, Wu F-X, Zhang A, Pedrycz W. Protein complex identification through Markov clustering with firefly algorithm on dynamic protein-protein interaction networks. Inf Sci. 2016;329:303\u201316.","journal-title":"Inf Sci"},{"issue":"7084","key":"2649_CR11","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1038\/nature04532","volume":"440","author":"A-C Gavin","year":"2006","unstructured":"Gavin A-C, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B, et al. Proteome survey reveals modularity of the yeast cell machinery. Nature. 2006;440(7084):631\u20136.","journal-title":"Nature"},{"issue":"2","key":"2649_CR12","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1089\/cmb.2008.01TT","volume":"16","author":"HCM Leung","year":"2009","unstructured":"Leung HCM, Xiang Q, Yiu SM, Chin FYL. Predicting protein complexes from PPI data: a core-attachment approach. J Comput Biol. 2009;16(2):133\u201344.","journal-title":"J Comput Biol"},{"key":"2649_CR13","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1186\/1471-2105-10-169","volume":"10","author":"M Wu","year":"2009","unstructured":"Wu M, Li X, Kwoh C-K, Ng S-K. A core-attachment based method to detect protein complexes in PPI networks. BMC Bioinformatics. 2009;10:169.","journal-title":"BMC Bioinformatics."},{"issue":"10","key":"2649_CR14","doi-asserted-by":"publisher","first-page":"e0186134","DOI":"10.1371\/journal.pone.0186134","volume":"12","author":"X Shen","year":"2017","unstructured":"Shen X, Yi L, Jiang X, He T, Yang J, Xie W, Hu P, Hu X. Identifying protein complex by integrating characteristic of core-attachment into dynamic PPI network. PLoS One. 2017;12(10):e0186134.","journal-title":"PLoS One"},{"issue":"3","key":"2649_CR15","doi-asserted-by":"publisher","first-page":"729","DOI":"10.1109\/TCBB.2013.86","volume":"10","author":"Y Zhang","year":"2013","unstructured":"Zhang Y, Lin H, Yang Z, Wang J, Li Y, Xu B. Protein complex prediction in large ontology attributed protein-protein interaction networks. IEEE\/ACM Transactions on Computational Biology and Bioinformatics. 2013;10(3):729\u201341.","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics."},{"issue":"11","key":"2649_CR16","doi-asserted-by":"publisher","first-page":"2023","DOI":"10.1002\/prot.24365","volume":"81","author":"M Wu","year":"2013","unstructured":"Wu M, Xie Z, Li X, Kwoh C-K, Zheng J. Identifying protein complexes from heterogeneous biological data. Proteins-Structure Function and Bioinformatics. 2013;81(11):2023\u201333.","journal-title":"Proteins-Structure Function and Bioinformatics"},{"issue":"2","key":"2649_CR17","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1109\/TNB.2014.2317519","volume":"13","author":"JM Zhao","year":"2014","unstructured":"Zhao JM, Hu XH, He TT, Li P, Zhang M, Shen XJ. An edge-based protein complex identification algorithm with gene co-expression data (PCIA-GeCo). IEEE Transactions on Nanobioscience. 2014;13(2):80\u20138.","journal-title":"IEEE Transactions on Nanobioscience"},{"issue":"7","key":"2649_CR18","doi-asserted-by":"publisher","first-page":"e0180570","DOI":"10.1371\/journal.pone.0180570","volume":"12","author":"HF Zhou","year":"2017","unstructured":"Zhou HF, Liu J, Li JH, Duan WC. A density-based approach for detecting complexes in weighted PPI networks by semantic similarity. PLoS One. 2017;12(7):e0180570.","journal-title":"PLoS One"},{"key":"2649_CR19","first-page":"240","volume-title":"Flower pollination algorithm for global optimization","author":"X-S Yang","year":"2012","unstructured":"Yang X-S. Flower pollination algorithm for global optimization. Berlin: Heidelberg. Springer Berlin Heidelberg; 2012. p. 240\u20139."},{"issue":"1","key":"2649_CR20","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ipl.2015.08.007","volume":"116","author":"R Wang","year":"2016","unstructured":"Wang R, Zhou Y, Qiao S, Huang K. Flower pollination algorithm with bee pollinator for cluster analysis. Inf Process Lett. 2016;116(1):1\u201314.","journal-title":"Inf Process Lett"},{"issue":"4","key":"2649_CR21","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1186\/s12918-018-0573-y","volume":"12","author":"X Lei","year":"2018","unstructured":"Lei X, Fang M, Wu F-X, Chen L. Improved flower pollination algorithm for identifying essential proteins. BMC Syst Biol. 2018;12(4):46.","journal-title":"BMC Syst Biol"},{"key":"2649_CR22","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1186\/1471-2105-15-335","volume":"15","author":"L Ou-Yang","year":"2014","unstructured":"Ou-Yang L, Dai DQ, Li XL, Wu M, Zhang XF, Yang P. Detecting temporal protein complexes from dynamic protein-protein interaction networks. BMC Bioinformatics. 2014;15:335.","journal-title":"BMC Bioinformatics"},{"key":"2649_CR23","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1186\/s12859-016-1101-y","volume":"17","author":"YJ Zhang","year":"2016","unstructured":"Zhang YJ, Lin HF, Yang ZH, Wang J, Liu YW, Sang ST. A method for predicting protein complex in dynamic PPI networks. BMC Bioinformatics. 2016;17:229.","journal-title":"BMC Bioinformatics."},{"key":"2649_CR24","doi-asserted-by":"crossref","unstructured":"Li M, Meng X, Zheng R, Wu FX, Li Y, Pan Y, Wang J. Identification of protein complexes by using a spatial and temporal active protein interaction network. IEEE\/ACM Transactions on Computational Biology and Bioinformatics. 2017:1\u20131.","DOI":"10.1109\/TCBB.2017.2749571"},{"issue":"2","key":"2649_CR25","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1002\/pmic.201200277","volume":"13","author":"JX Wang","year":"2013","unstructured":"Wang JX, Peng XQ, Li M, Pan Y. Construction and application of dynamic protein interaction network based on time course gene expression data. Proteomics. 2013;13(2):301\u201312.","journal-title":"Proteomics"},{"issue":"2","key":"2649_CR26","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1109\/TNB.2016.2536161","volume":"15","author":"B Zhao","year":"2016","unstructured":"Zhao B, Wang J, Li M, Li X, Li Y, Wu FX, Pan Y. A new method for predicting protein functions from dynamic weighted interactome networks. IEEE Trans Nanobioscience. 2016;15(2):131\u20139.","journal-title":"IEEE Trans Nanobioscience"},{"issue":"1","key":"2649_CR27","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1093\/nar\/30.1.303","volume":"30","author":"I Xenarios","year":"2002","unstructured":"Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, Eisenberg DDIP. The database of interacting proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 2002;30(1):303\u20135.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"2649_CR28","doi-asserted-by":"publisher","first-page":"D436","DOI":"10.1093\/nar\/gkj003","volume":"34","author":"U Guldener","year":"2006","unstructured":"Guldener U, Munsterkotter M, Oesterheld M, Pagel P, Ruepp A, Mewes HW, Stumpflen V. MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res. 2006;34(Database issue):D436\u201341.","journal-title":"Nucleic Acids Res"},{"issue":"7084","key":"2649_CR29","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1038\/nature04670","volume":"440","author":"NJ Krogan","year":"2006","unstructured":"Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 2006;440(7084):637\u201343.","journal-title":"Nature"},{"issue":"5751","key":"2649_CR30","doi-asserted-by":"publisher","first-page":"1152","DOI":"10.1126\/science.1120499","volume":"310","author":"BP Tu","year":"2005","unstructured":"Tu BP, Kudlicki A, Rowicka M, McKnight SL. Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science (New York, NY). 2005;310(5751):1152\u20138.","journal-title":"Science (New York, NY)"},{"key":"2649_CR31","first-page":"bau012","volume":"2014","author":"JX Binder","year":"2014","unstructured":"Binder JX, Pletscher-Frankild S, Tsafou K, Stolte C, O'Donoghue SI, Schneider R, Jensen LJ. COMPARTMENTS: unification and visualization of protein subcellular localization evidence. Database-the Journal of Biological Databases and Curation. 2014;2014:bau012.","journal-title":"Database-the Journal of Biological Databases and Curation"},{"issue":"1","key":"2649_CR32","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1093\/nar\/26.1.73","volume":"26","author":"JM Cherry","year":"1998","unstructured":"Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, et al. SGD: Saccharomyces genome database. Nucleic Acids Res. 1998;26(1):73\u20139.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"2649_CR33","doi-asserted-by":"publisher","first-page":"D169","DOI":"10.1093\/nar\/gkj148","volume":"34","author":"HW Mewes","year":"2006","unstructured":"Mewes HW, Frishman D, Mayer KF, Munsterkotter M, Noubibou O, Pagel P, Rattei T, Oesterheld M, Ruepp A, Stumpflen V. MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res. 2006;34(Database issue):D169\u201372.","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"2649_CR34","doi-asserted-by":"publisher","first-page":"D271","DOI":"10.1093\/nar\/gkh024","volume":"32","author":"R Zhang","year":"2004","unstructured":"Zhang R, Ou HY, Zhang CT. DEG: a database of essential genes. Nucleic Acids Res. 2004;32(Database issue):D271\u20132.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"2649_CR35","doi-asserted-by":"publisher","first-page":"825","DOI":"10.1093\/nar\/gkn1005","volume":"37","author":"SY Pu","year":"2009","unstructured":"Pu SY, Wong J, Turner B, Cho E, Wodak SJ. Up-to-date catalogues of yeast protein complexes. Nucleic Acids Res. 2009;37(3):825\u201331.","journal-title":"Nucleic Acids Res"},{"key":"2649_CR36","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1186\/1471-2105-7-207","volume":"7","author":"M Altaf-Ul-Amin","year":"2006","unstructured":"Altaf-Ul-Amin M, Shinbo Y, Mihara K, Kurokawa K, Kanaya S. Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics. 2006;7:207.","journal-title":"BMC Bioinformatics."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2649-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-019-2649-0\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2649-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,15]],"date-time":"2023-09-15T00:47:05Z","timestamp":1694738825000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-2649-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,3]]},"references-count":36,"journal-issue":{"issue":"S3","published-print":{"date-parts":[[2019,3]]}},"alternative-id":["2649"],"URL":"https:\/\/doi.org\/10.1186\/s12859-019-2649-0","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,3]]},"assertion":[{"value":"29 March 2019","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"131"}}